This Week in PLoS – Genome of a Dental Cavity Bacteria

National University of Ireland at Cork’s Douwe van Sinderen and his colleagues sequenced the genome of a dental cavity bacteria called Bifidobacterium dentium Bd1, finding features in it that help explain the bug’s propensity for living in the mouth and causing cavities. “[T]he genome of this opportunistic cariogen has evolved through a very limited number of horizontal gene acquisition events, highlighting the narrow boundaries that separate commensals from opportunistic pathogens,” the researchers write. A news story in our sister publication GenomeWeb Daily News has more details.

A California research team took a closer look at genetic variants involved several autoimmune diseases by doing a meta-analysis of genome-wide association studies. They found that certain autoimmune diseases cluster together and that SNPs that increase the risk of some conditions apparently protect against others. And, they say, the approach may be useful for better understanding autoimmune and many other types of disease. “As more GWA data becomes available, our method could be applied across tens or hundreds of diseases yielding the commonalities and differences in genetic architectures across all of human disease,” the team concludes.GenomeWeb Daily News also covered this story here.

An international research group used SNP markers to look at the genetic patterns and estimate linkage disequilibrium in 632 inbred maize lines from public breeding programs around the world in a PLoS ONE paper. After genotyping temperate, tropical, and sub-tropical lines, they applied more than 1,200 informative SNPs to examine everything from genetic diversity and population structure to familial relationships. They also did linkage disequilibrium analyses, showing that the LD distance increases when minor allele frequency increases, when sample size decreases, or in lines with lower genetic diversity (such as those from temperate regions).

French and Swiss researchers used a “Dirty Genome Approach” to find immunogenic proteins in unfinished genome sequences from an emerging human respiratory pathogen called Parachlamydia acanthamoebae using a combination of high-throughput, short-read sequencing and proteomics. Those involved say the proof-of-principle study highlights the potential of unfinished genomes — suggesting they can help guide antigen and DNA-based diagnostic tests for newly discovered pathogens.